+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16331 | |||||||||
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タイトル | RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Mammalian PIC / +1 nucleosome / transcription initiation / TRANSCRIPTION | |||||||||
機能・相同性 | 機能・相同性情報 MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / ventricular system development ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / ventricular system development / hair follicle maturation / RNA polymerase transcription factor SL1 complex / hair cell differentiation / snRNA transcription by RNA polymerase II / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / UV protection / transcription factor TFIIK complex / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA polymerase I core promoter sequence-specific DNA binding / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / transcription factor TFIIF complex / DNA 5'-3' helicase / RNA Polymerase III Abortive And Retractive Initiation / G protein-coupled receptor internalization / adult heart development / transcription factor TFIIA complex / female germ cell nucleus / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / male pronucleus / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / germinal vesicle / DNA 3'-5' helicase / [RNA-polymerase]-subunit kinase / transcription preinitiation complex / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / Signaling by FGFR2 IIIa TM / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / 3'-5' DNA helicase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIID complex / bone mineralization / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / spinal cord development / protein acetylation / cell division site / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Sus scrofa (ブタ) / Xenopus laevis (アフリカツメガエル) / unidentified adenovirus (ウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.1 Å | |||||||||
データ登録者 | Abril-Garrido J / Dienemann C / Grabbe F / Velychko T / Lidschreiber M / Wang H / Cramer P | |||||||||
資金援助 | ドイツ, European Union, 2件
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引用 | ジャーナル: Mol Cell / 年: 2023 タイトル: Structural basis of transcription reduction by a promoter-proximal +1 nucleosome. 著者: Julio Abril-Garrido / Christian Dienemann / Frauke Grabbe / Taras Velychko / Michael Lidschreiber / Haibo Wang / Patrick Cramer / 要旨: At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further ...At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further upstream, at a promoter-proximal location. Here, we establish a model system to show that a promoter-proximal +1 nucleosome can reduce RNA synthesis in vivo and in vitro, and we analyze its structural basis. We find that the PIC assembles normally when the edge of the +1 nucleosome is located 18 base pairs (bp) downstream of the transcription start site (TSS). However, when the nucleosome edge is located further upstream, only 10 bp downstream of the TSS, the PIC adopts an inhibited state. The transcription factor IIH (TFIIH) shows a closed conformation and its subunit XPB contacts DNA with only one of its two ATPase lobes, inconsistent with DNA opening. These results provide a mechanism for nucleosome-dependent regulation of transcription initiation. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_16331.map.gz | 202.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-16331-v30.xml emd-16331.xml | 71.2 KB 71.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_16331_fsc.xml | 14.2 KB | 表示 | FSCデータファイル |
画像 | emd_16331.png | 86.3 KB | ||
マスクデータ | emd_16331_msk_1.map | 244.1 MB | マスクマップ | |
Filedesc metadata | emd-16331.cif.gz | 16.6 KB | ||
その他 | emd_16331_half_map_1.map.gz emd_16331_half_map_2.map.gz | 193.7 MB 193.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16331 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16331 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_16331_validation.pdf.gz | 859.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_16331_full_validation.pdf.gz | 858.9 KB | 表示 | |
XML形式データ | emd_16331_validation.xml.gz | 21.5 KB | 表示 | |
CIF形式データ | emd_16331_validation.cif.gz | 28.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16331 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16331 | HTTPS FTP |
-関連構造データ
関連構造データ | 8byqMC 8bvwC 8bz1C C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_16331.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | emd_16331_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_16331_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_16331_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : RNA polymerase II pre-initiation complex with the proximal +1 nuc...
+超分子 #1: RNA polymerase II pre-initiation complex with the proximal +1 nuc...
+超分子 #2: General transcription factor IIH
+超分子 #3: Mammalian RNA polymerase II
+超分子 #4: Nucleosome (protein)
+超分子 #5: Nucleosome (DNA)
+超分子 #6: General transcription factor IIB
+超分子 #7: TATA-box binding protein
+超分子 #8: General transcription factor IIF
+超分子 #9: General transcription factor IIA
+超分子 #10: General transcription factor IIE
+分子 #1: General transcription and DNA repair factor IIH helicase subunit XPB
+分子 #2: TFIIH basal transcription factor complex helicase XPD subunit
+分子 #3: General transcription factor IIH subunit 1
+分子 #4: General transcription factor IIH subunit 4
+分子 #5: General transcription factor IIH subunit 2
+分子 #6: General transcription factor IIH subunit 3
+分子 #7: General transcription factor IIH subunit 5
+分子 #8: CDK-activating kinase assembly factor MAT1
+分子 #9: Cyclin-dependent kinase 7
+分子 #10: Cyclin-H
+分子 #11: DNA-directed RNA polymerase subunit
+分子 #12: DNA-directed RNA polymerase subunit beta
+分子 #13: DNA-directed RNA polymerase II subunit RPB3
+分子 #14: RNA polymerase II subunit D
+分子 #15: DNA-directed RNA polymerase II subunit E
+分子 #16: DNA-directed RNA polymerase II subunit F
+分子 #17: DNA-directed RNA polymerase II subunit RPB7
+分子 #18: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #19: DNA-directed RNA polymerase II subunit RPB9
+分子 #20: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #21: DNA-directed RNA polymerase II subunit RPB11-a
+分子 #22: RNA polymerase II subunit K
+分子 #23: Transcription initiation factor IIB
+分子 #25: TATA-box-binding protein
+分子 #26: General transcription factor IIF subunit 1
+分子 #27: General transcription factor IIF subunit 2
+分子 #29: Transcription initiation factor IIA subunit 1
+分子 #30: Transcription initiation factor IIA subunit 2
+分子 #31: General transcription factor IIE subunit 1
+分子 #32: Transcription initiation factor IIE subunit beta
+分子 #33: Histone H3.2
+分子 #34: Histone H4
+分子 #35: Histone H2A type 1
+分子 #36: Histone H2B 1.1
+分子 #24: Non-template DNA
+分子 #28: Template DNA
+分子 #37: IRON/SULFUR CLUSTER
+分子 #38: ZINC ION
+分子 #39: MAGNESIUM ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.5 |
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グリッド | モデル: Quantifoil R3.5/1 / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 3 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Quantum LS / エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 実像数: 36478 / 平均露光時間: 3.0 sec. / 平均電子線量: 50.45 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 1.3 µm / 最小 デフォーカス(公称値): 0.6 µm / 倍率(公称値): 81000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
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得られたモデル | PDB-8byq: |